Alternative splicing is important for increasing the complexity of the human proteome from a limited genome. Previous studies have shown that for some autoantigens, there is differential immunogenicity among alternatively spliced isoforms. In this report, we tested the hypothesis that alternative splicing is a common feature for transcripts of autologous proteins that are autoantigens. The corollary hypothesis tested was that non-autoantigen transcripts have a lower frequency of alternative splicing. We compared the extent of alternative splicing within 45 randomly selected self-proteins associated with autoimmune diseases to 9554 randomly selected proteins encoded in human genome using bioinformatics analysis. Isoform specific regions that result from alternative splicing were studied for their potential to be epitopes for antibodies or T cell epitopes. Our results demonstrate for the first time that alternative splicing occurred in 100% of the autoantigen transcripts. This is significantly higher that the approximately 42% rate of alternative splicing observed in 9554 randomly selected human gene transcripts. In addition, the majority of isoform-specific regions of these autoantigens encoded MHC restricted T cell antigen epitopes and autoantibody binding epitopes. Furthermore, 80% of the autoantigen transcripts underwent non-canonical alternative splicing, which is also significantly higher than the less than 1% rate in randomly selected gene transcripts. These studies suggest that non-canonical alternative splicing may be an important mechanism for the generation of untolerized epitopes that may lead to autoimmunity. Furthermore, the product of a transcript that does not undergo alternative splicing is unlikely to be a target antigen in autoimmunity.